﻿<?xml version="1.0" encoding="utf-8" ?>
<AutomationTest>
  <!-- One line sequence node which is used for BVT test cases -->
  <OneLineSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT</Sequence>
      <Sequence>CCCCCCCCC</Sequence>
      <Sequence>TTTTT</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA</Sequence>
      <Sequence>CAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC</Sequence>
      <Sequence>AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <MUMAlignLength>5</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,1,4,5,3,5,2,5,5,7,8,6,8,9,9,10,11,12,4,16,16,16,10,17,12,18,18,12,21,21,9,23,9,23,6,24,19,25,26,27,18,30,18,30,13,31,13,31,1,31,2,33,11,35,11,35,35,36,32,38,38,38,42,38,42,42,42,44,45,40,47,36,47,7,49,24,51,24,51,51,54,25,55,25,55,25,55,55,55,55,58,64,65,63,65,62,65,61,65,60,65,59,65,65,65,56,66,68,70,71,69,71,71,71,71</EdgeStartIndexes>
    <EdgeEndIndexes>0,1,71,71,3,71,2,5,5,71,8,6,8,9,9,10,11,12,71,71,71,17,10,17,12,71,18,71,71,71,71,23,71,23,6,24,71,71,71,71,71,71,71,71,71,71,71,71,1,31,3,71,71,71,11,71,35,37,71,71,39,71,71,71,71,71,71,71,71,71,71,37,71,71,50,24,71,24,71,71,71,71,71,71,71,71,71,71,71,55,58,71,71,63,71,62,71,61,71,60,71,59,71,71,71,71,71,68,71,71,69,71,71,71,71</EdgeEndIndexes>
    <Nodes>5,7,0,12,0,0,3,16,12,25,33,7,12,16,43,25,47,49,0,7,55,16,49,64,59,72,7,10,78,35,76,84,86,37,94,96,98,100,102,59,0,111,55</Nodes>
    <FirstSequenceMumOrder>1,2,3,4,5,6,7,8,9</FirstSequenceMumOrder>
    <FirstSequenceStart>31,2,25,15,66,11,0,6,33</FirstSequenceStart>
    <Length>5,7,6,5,5,5,5,5,5</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6,7,8,9</SecondSequenceMumOrder>
    <SecondSequenceStart>0,10,84,98,101,142,143,191,195</SecondSequenceStart>
    <ExpectedSequences>AAAGGGA,AAAGGGA,CATTA,CATTA,CAAAA,TTTTT,ATGTT,ATGTT,GAATGC,GAATGC,CAAAA,CAAAA,GGATT,GGATT,GCAAA,GCAAA,TTACC,TTACC</ExpectedSequences>
  </OneLineSequence>
  <!-- Small size sequence node which is used for BVT test cases -->
  <SmallSizeSequence>
    <FilePath>TestUtils\Multi_Seq_Small_Size.fasta</FilePath>
    <SearchSequenceFilePath>TestUtils\Multi_Seq_Search_Small_Size.fasta</SearchSequenceFilePath>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>TestUtils\Small_Size_Start_Index.txt</EdgeStartIndexes>
    <EdgeEndIndexes>TestUtils\Small_Size_End_Index.txt</EdgeEndIndexes>
    <Nodes>TestUtils\Small_Size_Nodes.txt</Nodes>
    <FirstSequenceMumOrder>TestUtils\Small_Size_First_Mum_Order.txt</FirstSequenceMumOrder>
    <FirstSequenceStart>TestUtils\Small_Size_First_Seq_Start.txt</FirstSequenceStart>
    <Length>TestUtils\Small_Size_Length.txt</Length>
    <SecondSequenceMumOrder>TestUtils\Small_Size_Second_Mum_Order.txt</SecondSequenceMumOrder>
    <SecondSequenceStart>TestUtils\Small_Size_Second_Seq_Start.txt</SecondSequenceStart>
    <ExpectedSequences>TestUtils\Small_Size_Aligned_Seq.txt</ExpectedSequences>
  </SmallSizeSequence>
  <!--One Unique match sequences-->
  <OneUniqueMatchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTGCAAA</Sequence>
      <Sequence>TAGTAGTTCTGCTATATACATTTG</Sequence>
      <Sequence>GTTATCATGCGAACAATTCAACAGACACTGTAGA</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ClustFirstSequenceMumOrder>0,97,152</ClustFirstSequenceMumOrder>
    <ClustFirstSequenceStart>1,2,3</ClustFirstSequenceStart>
    <ClustLength>16,24,34</ClustLength>
    <ClustSecondSequenceMumOrder>0,0,0</ClustSecondSequenceMumOrder>
    <ClustSecondSequenceStart>1,2,3</ClustSecondSequenceStart>
    <ExpectedSequences>CAAAAGGGATTGCAAA,CAAAAGGGATTGCAAA,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG,GTTATCATGCGAACAATTCAACAGACACTGTAGA,GTTATCATGCGAACAATTCAACAGACACTGTAGA</ExpectedSequences>
  </OneUniqueMatchSequence>
  <!-- Two unique matches with out cross overlap -->
  <TwoUniqueMatchWithoutCrossOverlapSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAAGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATTACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTAGAAAAGAATGTAAC</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <AlphabetName>Dna</AlphabetName>
    <FirstSequenceMumOrder>1,2,3,4,5,6</FirstSequenceMumOrder>
    <FirstSequenceStart>0,42,69,113,140,194</FirstSequenceStart>
    <Length>28,26,26,26,16,16</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6</SecondSequenceMumOrder>
    <SecondSequenceStart>0,28,54,80,106,120</SecondSequenceStart>
    <ClustFirstSequenceMumOrder>0,42,69,113,140,194</ClustFirstSequenceMumOrder>
    <ClustFirstSequenceStart>1,2,3,4,5,6</ClustFirstSequenceStart>
    <ClustLength>28,26,26,26,16,16</ClustLength>
    <ClustSecondSequenceMumOrder>0,28,0,26,0,14</ClustSecondSequenceMumOrder>
    <ClustSecondSequenceStart>1,2,3,4,5,6</ClustSecondSequenceStart>
  </TwoUniqueMatchWithoutCrossOverlapSequence>
  <!-- Two unique matches with cross overlap -->
  <TwoUniqueMatchWithCrossOverlapSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CCGGCTAGGAGGAGTAGTACAAAGGAGCCCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACACTGTAGACACAGTACTAGAAAAGAATGTAACCATTATGTATAGGTTATCATGCGA</Sequence>
      <Sequence>TCTGCTATATACATTTGCAACAAAAGCAACAAAAATGAAGGCAAT</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MUMAlignLength>8</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <FirstSequenceMumOrder>1,2,3,4,5,6,7</FirstSequenceMumOrder>
    <FirstSequenceStart>40,40,176,140,104,75,69</FirstSequenceStart>
    <Length>28,28,34,24,21,9,26</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6,7</SecondSequenceMumOrder>
    <SecondSequenceStart>0,28,56,90,114,130,133</SecondSequenceStart>
    <ClustFirstSequenceMumOrder>40,40,69,75,140,176</ClustFirstSequenceMumOrder>
    <ClustFirstSequenceStart>1,2,7,6,4,3</ClustFirstSequenceStart>
    <ClustLength>28,28,26,9,24,34</ClustLength>
    <ClustSecondSequenceMumOrder>0,28,19,16,3,40</ClustSecondSequenceMumOrder>
    <ClustSecondSequenceStart>1,2,7,6,4,3</ClustSecondSequenceStart>
    <ExpectedSequences>CCGGCTAGGAGGAGTAGTACAAAGGAGC,CCGGCTAGGAGGAGTAGTACAAAGGAGC,CCGGCTAGGAGGAGTAGTACAAAGGAGC,CCGGCTAGGAGGAGTAGTACAAAGGAGC,CATTATGTATAGGTTATCATGCGA,CATTATGTATAGGTTATCATGCGA,ACACTGTAGACACAGTACTAGAAAAGAATGTAAC,ACACTGTAGACACAGTACTAGAAAAGAATGTAAC,ACAAAAGCAACAAAAATGAAGGCAAT,ACAAAAGCAACAAAAATGAAGGCAAT,GCAACAAAA,GCAACAAAA,TCTGCTATATACATTTGCAAC,TCTGCTATATACATTTGCAAC</ExpectedSequences>
  </TwoUniqueMatchWithCrossOverlapSequence>
  <!-- Dna sequence node which is used for P1 test cases -->
  <DnaNucmerSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT</Sequence>
      <Sequence>CCCCCCCCC</Sequence>
      <Sequence>TTTTT</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA</Sequence>
      <Sequence>CAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC</Sequence>
      <Sequence>AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,1,4,5,3,5,2,5,5,7,8,6,8,9,9,10,11,12,4,16,16,16,10,17,12,18,18,12,21,21,9,23,9,23,6,24,19,25,26,27,18,30,18,30,13,31,13,31,1,31,2,33,11,35,11,35,35,36,32,38,38,38,42,38,42,42,42,44,45,40,47,36,47,7,49,24,51,24,51,51,54,25,55,25,55,25,55,55,55,55,58,64,65,63,65,62,65,61,65,60,65,59,65,65,65,56,66,68,70,71,69,71,71,71,71</EdgeStartIndexes>
    <EdgeEndIndexes>0,1,71,71,3,71,2,5,5,71,8,6,8,9,9,10,11,12,71,71,71,17,10,17,12,71,18,71,71,71,71,23,71,23,6,24,71,71,71,71,71,71,71,71,71,71,71,71,1,31,3,71,71,71,11,71,35,37,71,71,39,71,71,71,71,71,71,71,71,71,71,37,71,71,50,24,71,24,71,71,71,71,71,71,71,71,71,71,71,55,58,71,71,63,71,62,71,61,71,60,71,59,71,71,71,71,71,68,71,71,69,71,71,71,71</EdgeEndIndexes>
    <Nodes>5,7,0,12,0,0,3,16,12,25,33,7,12,16,43,25,47,49,0,7,55,16,49,64,59,72,7,10,78,35,76,84,86,37,94,96,98,100,102,59,0,111,55</Nodes>
    <FirstSequenceMumOrder>1,2,3,4,5,6,7,8,9</FirstSequenceMumOrder>
    <FirstSequenceStart>31,2,25,15,66,11,0,6,33</FirstSequenceStart>
    <Length>5,7,6,5,5,5,5,5,5</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6,7,8,9</SecondSequenceMumOrder>
    <SecondSequenceStart>0,10,84,98,101,142,143,191,195</SecondSequenceStart>
    <ExpectedSequences>AAAGGGA,AAAGGGA,CATTA,CATTA,CAAAA,TTTTT,ATGTT,ATGTT,GAATGC,GAATGC,CAAAA,CAAAA,GGATT,GGATT,GCAAA,GCAAA,TTACC,TTACC</ExpectedSequences>
  </DnaNucmerSequence>
  <!-- Rna sequence node which is used for P1 test cases -->
  <RnaNucmerSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGAUUGCAAAUGUUGGAGUGAAUGCCAUUACCUACCGGCUAGGAGGAGU</Sequence>
      <Sequence>CCCCCCCCC</Sequence>
      <Sequence>UUUUU</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAUUAAUGAUAAAGGGAAAGAAGUCCUCGUGCUAUGGGGCAUUCACCAUCCAUCUACUAGUGCUGACCAA</Sequence>
      <Sequence>CAAAGUCUCUAUCAGAAUGCAGAUGCAUAUGUUUUUGUGGGGUCAUCAAGAUAUAGCAAGAAGUUCAAGC</Sequence>
      <Sequence>AAGCAAAAUUAAACAGAGAAGAAAUAGAUGGGGUAAAGCUGGAAUCAACAAGGAUUUACCAGAUUUUGGC</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Rna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Rna</AlphabetName>
    <EdgeStartIndexes>0,1,4,5,3,5,2,5,5,7,8,6,8,9,9,10,11,12,4,16,16,16,10,17,12,18,18,12,21,21,9,23,9,23,6,24,19,25,26,27,18,30,18,30,13,31,13,31,1,31,2,33,11,35,11,35,35,36,32,38,38,38,42,38,42,42,42,44,45,40,47,36,47,7,49,24,51,24,51,51,54,25,55,25,55,25,55,55,55,55,58,64,65,63,65,62,65,61,65,60,65,59,65,65,65,56,66,68,70,71,69,71,71,71,71</EdgeStartIndexes>
    <EdgeEndIndexes>0,1,71,71,3,71,2,5,5,71,8,6,8,9,9,10,11,12,71,71,71,17,10,17,12,71,18,71,71,71,71,23,71,23,6,24,71,71,71,71,71,71,71,71,71,71,71,71,1,31,3,71,71,71,11,71,35,37,71,71,39,71,71,71,71,71,71,71,71,71,71,37,71,71,50,24,71,24,71,71,71,71,71,71,71,71,71,71,71,55,58,71,71,63,71,62,71,61,71,60,71,59,71,71,71,71,71,68,71,71,69,71,71,71,71</EdgeEndIndexes>
    <Nodes>5,7,0,12,0,0,3,16,12,25,33,7,12,16,43,25,47,49,0,7,55,16,49,64,59,72,7,10,78,35,76,84,86,37,94,96,98,100,102,59,0,111,55</Nodes>
    <FirstSequenceMumOrder>1,2,3,4,5,6,7,8,9</FirstSequenceMumOrder>
    <FirstSequenceStart>31,2,25,15,66,11,0,6,33</FirstSequenceStart>
    <Length>5,7,6,5,5,5,5,5,5</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6,7,8,9</SecondSequenceMumOrder>
    <SecondSequenceStart>0,10,84,98,101,142,143,191,195</SecondSequenceStart>
    <ExpectedSequences>AAAGGGA,AAAGGGA,CAUUA,CAUUA,CAAAA,UUUUU,AUGUU,AUGUU,GAAUGC,GAAUGC,CAAAA,CAAAA,GGAUU,GGAUU,GCAAA,GCAAA,UUACC,UUACC</ExpectedSequences>
  </RnaNucmerSequence>
  <!-- Medium size sequence node which is used for P1 test cases -->
  <MediumSizeSequence>
    <FilePath>TestUtils\Multi_Seq_Medium_Size.fasta</FilePath>
    <SearchSequenceFilePath>TestUtils\Multi_Seq_Search_Medium_Size.fasta</SearchSequenceFilePath>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <GapOpenCost>-10</GapOpenCost>
    <MUMLength>5</MUMLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>8</MUMAlignLength>
    <ClustCount1>570</ClustCount1>
    <ClustCount2>518</ClustCount2>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>TestUtils\Medium_Size_Start_Index.txt</EdgeStartIndexes>
    <EdgeEndIndexes>TestUtils\Medium_Size_End_Index.txt</EdgeEndIndexes>
    <Nodes>TestUtils\Medium_Size_Nodes.txt</Nodes>
    <FirstSequenceMumOrder>TestUtils\Medium_Size_First_Mum_Order.txt</FirstSequenceMumOrder>
    <FirstSequenceStart>TestUtils\Medium_Size_First_Seq_Start.txt</FirstSequenceStart>
    <Length>TestUtils\Medium_Size_Length.txt</Length>
    <SecondSequenceMumOrder>TestUtils\Medium_Size_Second_Mum_Order.txt</SecondSequenceMumOrder>
    <SecondSequenceStart>TestUtils\Medium_Size_Second_Seq_Start.txt</SecondSequenceStart>
    <ExpectedSequences>TestUtils\Medium_Size_Aligned_Seq.txt</ExpectedSequences>
  </MediumSizeSequence>
  <!-- One line sequence node which is used for P1 test cases and which has repeating characters -->
  <OneLineRepeatingCharacters>
    <ReferenceSequences>
      <Sequence>GGGATTGCAAATGTTGGAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>TGCTATTAGAACTTAAAAAGCCTAAATAGCATAGATAAAAAAAAGGATTGCAAATAAAAAAAA</Sequence>
    </SearchSequences>
    <MUMLength>4</MUMLength>
    <MUMAlignLength>4</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,2,3,1,3,3,4,5,6,7,7,4,9,10,11,5,12,7,13,13,7,16,16,4,18,4,18,18,21,21,11,23,64,65,63,65,62,65,61,65,60,65,59,65,58,65,57,65,56,65,55,65,54,65,53,65,52,65,51,65,50,65,49,65,48,65,47,65,46,65,45,65,44,65,43,65,42,65,41,65,40,65,39,65,38,65,37,65,36,65,35,65,34,65,33,65,32,65,31,65,30,65,29,65,28,65,27,65,26,65,25,65,24,65,65,65,65,65</EdgeStartIndexes>
    <EdgeEndIndexes>0,65,3,1,3,3,4,6,6,65,65,4,9,10,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,23,65,65,63,65,62,65,61,65,60,65,59,65,58,65,57,65,56,65,55,65,54,65,53,65,52,65,51,65,50,65,49,65,48,65,47,65,46,65,45,65,44,65,43,65,42,65,41,65,40,65,39,65,38,65,37,65,36,65,35,65,34,65,33,65,32,65,31,65,30,65,29,65,28,65,27,65,26,65,25,65,24,65,65,65,65,65</EdgeEndIndexes>
    <Nodes>4,0,0,0,12,8,4,18,26,12,14,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,31</Nodes>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>8,17,1</FirstSequenceStart>
    <Length>4,4,11</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>23,43,44</SecondSequenceStart>
    <ExpectedSequences>GGATTGCAAAT,GGATTGCAAAT,AAAT,AAAT,AGGA,AGGA</ExpectedSequences>
  </OneLineRepeatingCharacters>
  <!-- One line sequence node which is used for P1 test cases and which has repeating characters -->
  <OneLineAlternateRepeatingCharacters>
    <ReferenceSequences>
      <Sequence>GGAATTGCAAATGTTGGAGGATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>TGCTATTAGAACTTAAAGCCTAAATAGCATAGATAAAAAAGGAATTGCAAATGTTGGAGGATATATATATATATATAAGGAATTGAGGAATTGAGGAATTG</Sequence>
    </SearchSequences>
    <GapOpenCost>-10</GapOpenCost>
    <MUMLength>6</MUMLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>15</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,1,2,2,3,4,4,5,6,7,7,4,10,5,12,5,12,7,13,13,7,16,16,3,18,3,18,18,21,21,22,22,106,108,106,108,104,108,104,108,102,108,102,108,100,108,100,108,98,108,98,108,96,108,96,108,94,108,94,108,92,108,92,108,90,108,90,108,88,108,88,108,86,108,86,108,84,108,84,108,82,108,82,108,80,108,80,108,78,108,78,108,76,108,76,108,74,108,74,108,72,108,72,108,70,108,70,108,68,108,68,108,66,108,66,108,64,108,64,108,62,108,62,108,60,108,60,108,58,108,58,108,56,108,56,108,54,108,54,108,52,108,52,108,50,108,50,108,48,108,48,108,46,108,46,108,44,108,44,108,42,108,42,108,40,108,40,108,38,108,38,108,36,108,36,108,34,108,34,108,32,108,32,108,30,108,30,108,28,108,28,108,26,108,26,108,24,108,24,108,108,108,108</EdgeStartIndexes>
    <EdgeEndIndexes>0,2,2,2,3,4,4,6,6,108,108,4,108,108,108,108,108,108,108,108,108,108,108,108,108,108,108,108,108,108,23,23,108,108,108,108,105,108,105,108,103,108,103,108,101,108,101,108,99,108,99,108,97,108,97,108,95,108,95,108,93,108,93,108,91,108,91,108,89,108,89,108,87,108,87,108,85,108,85,108,83,108,83,108,81,108,81,108,79,108,79,108,77,108,77,108,75,108,75,108,73,108,73,108,71,108,71,108,69,108,69,108,67,108,67,108,65,108,65,108,63,108,63,108,61,108,61,108,59,108,59,108,57,108,57,108,55,108,55,108,53,108,53,108,51,108,51,108,49,108,49,108,47,108,47,108,45,108,45,108,43,108,43,108,41,108,41,108,39,108,39,108,37,108,37,108,35,108,35,108,33,108,33,108,31,108,31,108,29,108,29,108,27,108,27,108,25,108,25,108,108,108,108</EdgeEndIndexes>
    <Nodes>0,0,0,5,16,8,2,18,26,5,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,115,117,119,121,123,125,127,129,131,133,135,137,139,141,143,145,147,149,151,153,155,157,159,161,163,165,167,169,171,173,175,177,179,181,183,185,187,189,191,193,195,197,199,16</Nodes>
    <ExpectedSequences>GGAATTGCAAATGTTGGAGGATATATATATATATATA,GGAATTGCAAATGTTGGAGGATATATATATATATATA</ExpectedSequences>
  </OneLineAlternateRepeatingCharacters>
  <!-- One line sequence node which is used for P1 test cases and which has only repeating characters -->
  <OneLineOnlyRepeatingCharacters>
    <ReferenceSequences>
      <Sequence>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>TGCTATTAGAACTTAAAGCCTAAATAGCATAGATAAAAAA</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <GapOpenCost>-10</GapOpenCost>
    <MUMLength>6</MUMLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>20</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,68,69,67,69,66,69,65,69,64,69,63,69,62,69,61,69,60,69,59,69,58,69,57,69,56,69,55,69,54,69,53,69,52,69,51,69,50,69,49,69,48,69,47,69,46,69,45,69,44,69,43,69,42,69,41,69,40,69,39,69,38,69,37,69,36,69,35,69,34,69,33,69,32,69,31,69,30,69,29,69,28,69,27,69,26,69,25,69,24,69,23,69,22,69,21,69,20,69,19,69,18,69,17,69,16,69,15,69,14,69,13,69,12,69,11,69,10,69,9,69,8,69,7,69,6,69,5,69,4,69,3,69,2,69,1,69,69</EdgeStartIndexes>
    <EdgeEndIndexes>0,69,69,67,69,66,69,65,69,64,69,63,69,62,69,61,69,60,69,59,69,58,69,57,69,56,69,55,69,54,69,53,69,52,69,51,69,50,69,49,69,48,69,47,69,46,69,45,69,44,69,43,69,42,69,41,69,40,69,39,69,38,69,37,69,36,69,35,69,34,69,33,69,32,69,31,69,30,69,29,69,28,69,27,69,26,69,25,69,24,69,23,69,22,69,21,69,20,69,19,69,18,69,17,69,16,69,15,69,14,69,13,69,12,69,11,69,10,69,9,69,8,69,7,69,6,69,5,69,4,69,3,69,2,69,1,69,69</EdgeEndIndexes>
    <Nodes>4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,80,82,84,86,88,90,92,94,96,98,100,102,104,106,108,110,112,114,116,118,120,122,124,126,128,130,132,134,136,0</Nodes>
    <ExpectedSequences></ExpectedSequences>
  </OneLineOnlyRepeatingCharacters>
  <!-- Dna sequence node for FastA file which is used for validating Dna Sequences -->
  <SimpleDnaFasta>
    <FilePath>TestUtils\Multi_Seq_Small_Size.fasta</FilePath>
    <SearchSequenceFilePath>TestUtils\Multi_Seq_Search_Small_Size.fasta</SearchSequenceFilePath>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>TestUtils\Small_Size_Start_Index.txt</EdgeStartIndexes>
    <EdgeEndIndexes>TestUtils\Small_Size_End_Index.txt</EdgeEndIndexes>
    <Nodes>TestUtils\Small_Size_Nodes.txt</Nodes>
    <FirstSequenceMumOrder>TestUtils\Small_Size_First_Mum_Order.txt</FirstSequenceMumOrder>
    <FirstSequenceStart>TestUtils\Small_Size_First_Seq_Start.txt</FirstSequenceStart>
    <Length>TestUtils\Small_Size_Length.txt</Length>
    <SecondSequenceMumOrder>TestUtils\Small_Size_Second_Mum_Order.txt</SecondSequenceMumOrder>
    <SecondSequenceStart>TestUtils\Small_Size_Second_Seq_Start.txt</SecondSequenceStart>
    <ExpectedSequences>TestUtils\Small_Size_Aligned_Seq.txt</ExpectedSequences>
  </SimpleDnaFasta>
  <!-- Dna sequence node for GenBank file which is used for validating Dna Sequences -->
  <SimpleDnaGenBank>
    <FilePath>TestUtils\Nucmer_Reference_Seq.gbk</FilePath>
    <SearchSequenceFilePath>TestUtils\Nucmer_Query_Seq.gbk</SearchSequenceFilePath>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>4</MUMLength>
    <MUMAlignLength>4</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,2,3,1,3,3,4,5,6,7,7,4,9,10,11,5,12,7,13,13,7,16,16,4,18,4,18,18,21,21,11,23,59,60,58,60,57,60,56,60,55,60,54,60,53,60,52,60,51,60,50,60,49,60,48,60,47,60,46,60,45,60,44,60,43,60,42,60,41,60,40,60,39,60,38,60,37,60,36,60,35,60,34,60,33,60,32,60,31,60,30,60,29,60,28,60,27,60,26,60,25,60,24,60,60,60,60,60</EdgeStartIndexes>
    <EdgeEndIndexes>0,60,3,1,3,3,4,6,6,60,60,4,9,10,60,60,60,60,60,60,60,60,60,60,60,60,60,60,60,60,60,23,60,60,58,60,57,60,56,60,55,60,54,60,53,60,52,60,51,60,50,60,49,60,48,60,47,60,46,60,45,60,44,60,43,60,42,60,41,60,40,60,39,60,38,60,37,60,36,60,35,60,34,60,33,60,32,60,31,60,30,60,29,60,28,60,27,60,26,60,25,60,24,60,60,60,60,60</EdgeEndIndexes>
    <Nodes>4,0,0,0,12,8,4,18,26,12,14,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,31</Nodes>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>8,17,1</FirstSequenceStart>
    <Length>4,4,11</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>23,43,44</SecondSequenceStart>
    <ExpectedSequences>GGATTGCAAA,GGATTGCAAA,AAAT,AAAT,AGGA,AGGA</ExpectedSequences>
  </SimpleDnaGenBank>
  <!-- Dna sequence node for Gff file which is used for validating Dna Sequences -->
  <SimpleDnaGff>
    <FilePath>TestUtils\Nucmer_Reference_Seq.gff</FilePath>
    <SearchSequenceFilePath>TestUtils\Nucmer_Query_Seq.gff</SearchSequenceFilePath>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>4</MUMLength>
    <MUMAlignLength>4</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,2,3,1,3,3,4,5,6,7,7,4,9,10,11,5,12,7,13,13,7,16,16,4,18,4,18,18,21,21,11,23,64,65,63,65,62,65,61,65,60,65,59,65,58,65,57,65,56,65,55,65,54,65,53,65,52,65,51,65,50,65,49,65,48,65,47,65,46,65,45,65,44,65,43,65,42,65,41,65,40,65,39,65,38,65,37,65,36,65,35,65,34,65,33,65,32,65,31,65,30,65,29,65,28,65,27,65,26,65,25,65,24,65,65,65,65,65</EdgeStartIndexes>
    <EdgeEndIndexes>0,65,3,1,3,3,4,6,6,65,65,4,9,10,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,23,65,65,63,65,62,65,61,65,60,65,59,65,58,65,57,65,56,65,55,65,54,65,53,65,52,65,51,65,50,65,49,65,48,65,47,65,46,65,45,65,44,65,43,65,42,65,41,65,40,65,39,65,38,65,37,65,36,65,35,65,34,65,33,65,32,65,31,65,30,65,29,65,28,65,27,65,26,65,25,65,24,65,65,65,65,65</EdgeEndIndexes>
    <Nodes>4,0,0,0,12,8,4,18,26,12,14,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79,81,83,85,87,89,91,93,95,97,99,101,103,105,107,109,111,113,31</Nodes>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>8,17,1</FirstSequenceStart>
    <Length>4,4,11</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>23,43,44</SecondSequenceStart>
    <ExpectedSequences>GGATTGCAAAT,GGATTGCAAAT,AAAT,AAAT,AGGA,AGGA</ExpectedSequences>
  </SimpleDnaGff>
  <!-- Same sequences-->
  <SameSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <AlphabetName>Dna</AlphabetName>
    <FirstSequenceMumOrder>1</FirstSequenceMumOrder>
    <FirstSequenceStart>0</FirstSequenceStart>
    <Length>68</Length>
    <SecondSequenceMumOrder>1</SecondSequenceMumOrder>
    <SecondSequenceStart>0</SecondSequenceStart>
    <ExpectedSequences>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC,CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</ExpectedSequences>
  </SameSequence>
  <!--One Unique match sequences-->
  <OneLineNoMatchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>TTTTTTT</Sequence>
      <Sequence>TTTTTTTTT</Sequence>
      <Sequence>TTTTTTTTTT</Sequence>
    </SearchSequences>
    <MUMLength>6</MUMLength>
    <MUMAlignLength>6</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <FirstSequenceMumOrder></FirstSequenceMumOrder>
    <FirstSequenceStart></FirstSequenceStart>
    <Length></Length>
    <SecondSequenceMumOrder></SecondSequenceMumOrder>
    <SecondSequenceStart></SecondSequenceStart>
    <ExpectedSequences></ExpectedSequences>
  </OneLineNoMatchSequence>
  <!--Dna with Ambiguity Characters in Reference sequences-->
  <DnaAmbiguityReferenceSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGCMGRS</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACASRG</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACMRS</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTGCAAA</Sequence>
      <Sequence>TAGTAGTTCTGCTATATACATTTG</Sequence>
      <Sequence>GTTATCATGCGAACAATTCAACAGACACTGTAGA</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <AlphabetName>ambiguousdna</AlphabetName>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>0,101,158</FirstSequenceStart>
    <Length>16,24,34</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>0,16,39</SecondSequenceStart>
    <ExpectedSequences>CAAAAGGGATTGCAAA,CAAAAGGGATTGCAAA,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG,GTTATCATGCGAACAATTCAACAGACACTGTAGA,GTTATCATGCGAACAATTCAACAGACACTGTAGA</ExpectedSequences>
  </DnaAmbiguityReferenceSequence>
  <!--Dna with Ambiguity Characters in Search sequences-->
  <DnaAmbiguitySearchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTGCAAA</Sequence>
      <Sequence>TAGTAGTTCTGCTATATACATTTGMGRS</Sequence>
      <Sequence>GTTATCATGCGAACAATTCAACAGACACTGTAGARMGS</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <AlphabetName>ambiguousdna</AlphabetName>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>0,97,152</FirstSequenceStart>
    <Length>16,24,34</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>0,16,44</SecondSequenceStart>
    <ExpectedSequences>CAAAAGGGATTGCAAA,CAAAAGGGATTGCAAA,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG,GTTATCATGCGAACAATTCAACAGACACTGTAGA,GTTATCATGCGAACAATTCAACAGACACTGTAGA</ExpectedSequences>
  </DnaAmbiguitySearchSequence>
  <!-- Rna with Ambiguity Characters in Reference sequences -->
  <RnaAmbiguityReferenceSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGAUUGCAAAUGUUGGAGUGAAUGCCAUUACCUACCGGCUAGGAGGAGUAGUACAAAGGAGCMGRS</Sequence>
      <Sequence>ACAAAAGCAACAAAAAUGAAGGCAAUACUAGUAGUUCUGCUAUAUACAUUUGCAACCGCAAAUGCAGACASRG</Sequence>
      <Sequence>CAUUAUGUAUAGGUUAUCAUGCGAACAAUUCAACAGACACUGUAGACACAGUACUAGAAAAGAAUGUAACMRS</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGAUUGCAAA</Sequence>
      <Sequence>UAGUAGUUCUGCUAUAUACAUUUG</Sequence>
      <Sequence>GUUAUCAUGCGAACAAUUCAACAGACACUGUAGA</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <AlphabetName>ambiguousrna</AlphabetName>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>0,101,159</FirstSequenceStart>
    <Length>16,24,34</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>0,16,39</SecondSequenceStart>
    <ExpectedSequences>CAAAAGGGAUUGCAAA,CAAAAGGGAUUGCAAA,UAGUAGUUCUGCUAUAUACAUUUG,UAGUAGUUCUGCUAUAUACAUUUG,GUUAUCAUGCGAACAAUUCAACAGACACUGUAGA,GUUAUCAUGCGAACAAUUCAACAGACACUGUAGA</ExpectedSequences>
  </RnaAmbiguityReferenceSequence>
  <!-- Rna with Ambiguity Characters in Search sequences -->
  <RnaAmbiguitySearchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGAUUGCAAAUGUUGGAGUGAAUGCCAUUACCUACCGGCUAGGAGGAGUAGUACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAAUGAAGGCAAUACUAGUAGUUCUGCUAUAUACAUUUGCAACCGCAAAUGCAGACA</Sequence>
      <Sequence>CAUUAUGUAUAGGUUAUCAUGCGAACAAUUCAACAGACACUGUAGACACAGUACUAGAAAAGAAUGUAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGAUUGCAAA</Sequence>
      <Sequence>UAGUAGUUCUGCUAUAUACAUUUGMGRS</Sequence>
      <Sequence>GUUAUCAUGCGAACAAUUCAACAGACACUGUAGARMGS</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <AlphabetName>ambiguousrna</AlphabetName>
    <FirstSequenceMumOrder>1,2,3</FirstSequenceMumOrder>
    <FirstSequenceStart>0,97,152</FirstSequenceStart>
    <Length>16,24,34</Length>
    <SecondSequenceMumOrder>1,2,3</SecondSequenceMumOrder>
    <SecondSequenceStart>0,16,44</SecondSequenceStart>
    <ExpectedSequences>CAAAAGGGAUUGCAAA,CAAAAGGGAUUGCAAA,UAGUAGUUCUGCUAUAUACAUUUG,UAGUAGUUCUGCUAUAUACAUUUG,GUUAUCAUGCGAACAAUUCAACAGACACUGUAGA,GUUAUCAUGCGAACAAUUCAACAGACACUGUAGA</ExpectedSequences>
  </RnaAmbiguitySearchSequence>
  <!-- Minimum Score Greater sequences-->
  <MinimumScoreGreaterSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTGCAAA</Sequence>
      <Sequence>TAGTAGTTCTGCTATATACATTTG</Sequence>
      <Sequence>GTTATCATGCGAACAATTCAACAGACACTGTAGA</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <MinimumScore>9</MinimumScore>
    <FixedSeparation>6</FixedSeparation>
    <MaximumSeparation>5</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ClustFirstSequenceMumOrder>0,97,152</ClustFirstSequenceMumOrder>
    <ClustFirstSequenceStart>0,97,151</ClustFirstSequenceStart>
    <ClustLength>16,24,34</ClustLength>
    <ClustSecondSequenceMumOrder>0,0,0</ClustSecondSequenceMumOrder>
    <ClustSecondSequenceStart>0,16,39</ClustSecondSequenceStart>
    <ExpectedSequences>CAAAAGGGATTGCAAA,CAAAAGGGATTGCAAA,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG,GTTATCATGCGAACAATTCAACAGACACTGTAGA,GTTATCATGCGAACAATTCAACAGACACTGTAGA</ExpectedSequences>
  </MinimumScoreGreaterSequence>
  <!-- One line sequence node which is used for P1 test cases -->
  <OneLineOneReferenceQuerySequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG</ExpectedSequences>
  </OneLineOneReferenceQuerySequence>
  <!-- Dna sequence node which is used for P1 test cases -->
  <SingleDnaNucmerSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>GCAAATGTTGGAGTGAATGCCA</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>GCAAATGTTGGAGTGAATGCCA,GCAAATGTTGGAGTGAATGCCA</ExpectedSequences>
  </SingleDnaNucmerSequence>
  <!-- Rna sequence node which is used for P1 test cases -->
  <SingleRnaNucmerSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGAUUGCAAAUGUUGGAGUGAAUGCCAUUACCUACCGGCUAGGAGGAGU</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGAUUGCAAAUGUUG</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Rna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Rna</AlphabetName>
    <ExpectedSequences>CAAAAGGGAUUGCAAAUGUUG,CAAAAGGGAUUGCAAAUGUUG</ExpectedSequences>
  </SingleRnaNucmerSequence>
  <!--Overlap match sequences-->
  <OneOverlapMatchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
      <Sequence>TAGTAGTTCTGCTATATACATTTG</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG</ExpectedSequences>
  </OneOverlapMatchSequence>
  <!--Multi reference single query sequences-->
  <MultiRefSingleQueryMatchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG</ExpectedSequences>
  </MultiRefSingleQueryMatchSequence>
  <GreaterMumLengthSequence>
    <ReferenceSequences>
      <Sequence>CAAAGGAGC</Sequence>
      <Sequence>AAATGCAGA</Sequence>
      <Sequence>TAGAAAAGA</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
      <Sequence>TATATACATTTG</Sequence>
    </SearchSequences>
    <MUMLength>50</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG</ExpectedSequences>
  </GreaterMumLengthSequence>
  <InvalidMumLengthSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
    </SearchSequences>
    <MUMLength>0</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG,TAGTAGTTCTGCTATATACATTTG,TAGTAGTTCTGCTATATACATTTG</ExpectedSequences>
  </InvalidMumLengthSequence>
  <!--Single reference Multiple query Dna sequences-->
  <SingleRefMultiQueryDnaMatchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG</ExpectedSequences>
  </SingleRefMultiQueryDnaMatchSequence>
  <!--Single reference Multiple query Rna sequences-->
  <SingleRefMultiQueryRnaMatchSequence>
    <ReferenceSequences>
      <Sequence>AUGCGAUUGCUAUUAGAACUUAAAGCCCUAAAUAGCAUAGAUAAAAAACAAUUAUCUAACUAUCUA</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>GCGAUUGCUAUUAG</Sequence>
      <Sequence>AACUUAAAGCCCUAAAUAGCAUAGAUAAAAAACAAUUAUCUAAC</Sequence>
      <Sequence>ACUUAAAGCCCUAAAUAGCA</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Rna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG</ExpectedSequences>
  </SingleRefMultiQueryRnaMatchSequence>
  <!--Multiple reference Multiple query Dna sequences-->
  <MultiRefMultiQueryDnaMatchSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGTAGTACAAAGGAGC</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAAAAGGGATTG</Sequence>
      <Sequence>ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA</Sequence>
      <Sequence>CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>CAAAAGGGATTG,CAAAAGGGATTG,ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA,ACAAAAGCAACAAAAATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACA,CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC,CATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAAC</ExpectedSequences>
  </MultiRefMultiQueryDnaMatchSequence>
  <!--Multiple reference Multiple query Rna sequences-->
  <MultiRefMultiQueryRnaMatchSequence>
    <ReferenceSequences>
      <Sequence>AUGCGAUUGCUAUUAGAACUUAAAGCCCUAAAUAGCAUAGAUAAAAAACAAUUAUCUAACUAUCUA</Sequence>
      <Sequence>UCUAACUAUCUAAUACAAGGUUUCAUUUAUAAUAUAUUAAAAAAUACCGAAUACUCU</Sequence>
      <Sequence>AUUAAAAAAUACCGAAUACUCUUGGUUACAUAAUUGGAAGAAAGAGAAAUAUUUUAAUUUUACCUUA</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>GCGAUUGCUAUUAG</Sequence>
      <Sequence>AACUUAAAGCCCUAAAUAGCAUAGAUAAAAAACAAUUAUCUAAC</Sequence>
      <Sequence>ACUUAAAGCCCUAAAUAGCA</Sequence>
    </SearchSequences>
    <MUMLength>8</MUMLength>
    <MUMAlignLength>8</MUMAlignLength>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <MaximumSeparation>0</MaximumSeparation>
    <SeparationFactor>0</SeparationFactor>
    <AlphabetName>Rna</AlphabetName>
    <ExpectedSequences>GCGAUUGCUAUUAG,GCGAUUGCUAUUAG,AACUUAAAGCCCUAAAUAGCAUAGAUAAAAAACAAUUAUCUAAC,AACUUAAAGCCCUAAAUAGCAUAGAUAAAAAACAAUUAUCUAAC,ACUUAAAGCCCUAAAUAGCA,ACUUAAAGCCCUAAAUAGCA</ExpectedSequences>
  </MultiRefMultiQueryRnaMatchSequence>
  <!-- Dna sequence node which is used for P1 test cases -->
  <SimpleAlignDnaNucmerSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGATTGCAAATGTTGGAGTGAATGCCATTACCTACCGGCTAGGAGGAGT</Sequence>
      <Sequence>CCCCCCCCC</Sequence>
      <Sequence>TTTTT</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAA</Sequence>
      <Sequence>CAAAGTCTCTATCAGAATGCAGATGCATATGTTTTTGTGGGGTCATCAAGATATAGCAAGAAGTTCAAGC</Sequence>
      <Sequence>AAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGC</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Dna</AlphabetName>
    <EdgeStartIndexes>0,1,4,5,3,5,2,5,5,7,8,6,8,9,9,10,11,12,4,16,16,16,10,17,12,18,18,12,21,21,9,23,9,23,6,24,19,25,26,27,18,30,18,30,13,31,13,31,1,31,2,33,11,35,11,35,35,36,32,38,38,38,42,38,42,42,42,44,45,40,47,36,47,7,49,24,51,24,51,51,54,25,55,25,55,25,55,55,55,55,58,64,65,63,65,62,65,61,65,60,65,59,65,65,65,56,66,68,70,71,69,71,71,71,71</EdgeStartIndexes>
    <EdgeEndIndexes>0,1,71,71,3,71,2,5,5,71,8,6,8,9,9,10,11,12,71,71,71,17,10,17,12,71,18,71,71,71,71,23,71,23,6,24,71,71,71,71,71,71,71,71,71,71,71,71,1,31,3,71,71,71,11,71,35,37,71,71,39,71,71,71,71,71,71,71,71,71,71,37,71,71,50,24,71,24,71,71,71,71,71,71,71,71,71,71,71,55,58,71,71,63,71,62,71,61,71,60,71,59,71,71,71,71,71,68,71,71,69,71,71,71,71</EdgeEndIndexes>
    <Nodes>5,7,0,12,0,0,3,16,12,25,33,7,12,16,43,25,47,49,0,7,55,16,49,64,59,72,7,10,78,35,76,84,86,37,94,96,98,100,102,59,0,111,55</Nodes>
    <FirstSequenceMumOrder>1,2,3,4,5,6,7,8,9</FirstSequenceMumOrder>
    <FirstSequenceStart>31,2,25,15,66,11,0,6,33</FirstSequenceStart>
    <Length>5,7,6,5,5,5,5,5,5</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6,7,8,9</SecondSequenceMumOrder>
    <SecondSequenceStart>0,10,84,98,101,142,143,191,195</SecondSequenceStart>
    <ExpectedSequences>AAAGGGA,AAAGGGA,CATTA,CATTA,CAAAAG,TTTTTG,ATGTT,ATGTT,GAATGC,GAATGC,CAAAA,CAAAA,GGATT,GGATT,GCAAA,GCAAA,TTACC,TTACC</ExpectedSequences>
  </SimpleAlignDnaNucmerSequence>
  <!-- Rna sequence node which is used for P1 test cases -->
  <SimpleAlignRnaNucmerSequence>
    <ReferenceSequences>
      <Sequence>CAAAAGGGAUUGCAAAUGUUGGAGUGAAUGCCAUUACCUACCGGCUAGGAGGAGU</Sequence>
      <Sequence>CCCCCCCCC</Sequence>
      <Sequence>UUUUU</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>CAUUAAUGAUAAAGGGAAAGAAGUCCUCGUGCUAUGGGGCAUUCACCAUCCAUCUACUAGUGCUGACCAA</Sequence>
      <Sequence>CAAAGUCUCUAUCAGAAUGCAGAUGCAUAUGUUUUUGUGGGGUCAUCAAGAUAUAGCAAGAAGUUCAAGC</Sequence>
      <Sequence>AAGCAAAAUUAAACAGAGAAGAAAUAGAUGGGGUAAAGCUGGAAUCAACAAGGAUUUACCAGAUUUUGGC</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Rna</SearchSequenceAlphabet>
    <MUMLength>5</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Rna</AlphabetName>
    <EdgeStartIndexes>0,1,4,5,3,5,2,5,5,7,8,6,8,9,9,10,11,12,4,16,16,16,10,17,12,18,18,12,21,21,9,23,9,23,6,24,19,25,26,27,18,30,18,30,13,31,13,31,1,31,2,33,11,35,11,35,35,36,32,38,38,38,42,38,42,42,42,44,45,40,47,36,47,7,49,24,51,24,51,51,54,25,55,25,55,25,55,55,55,55,58,64,65,63,65,62,65,61,65,60,65,59,65,65,65,56,66,68,70,71,69,71,71,71,71</EdgeStartIndexes>
    <EdgeEndIndexes>0,1,71,71,3,71,2,5,5,71,8,6,8,9,9,10,11,12,71,71,71,17,10,17,12,71,18,71,71,71,71,23,71,23,6,24,71,71,71,71,71,71,71,71,71,71,71,71,1,31,3,71,71,71,11,71,35,37,71,71,39,71,71,71,71,71,71,71,71,71,71,37,71,71,50,24,71,24,71,71,71,71,71,71,71,71,71,71,71,55,58,71,71,63,71,62,71,61,71,60,71,59,71,71,71,71,71,68,71,71,69,71,71,71,71</EdgeEndIndexes>
    <Nodes>5,7,0,12,0,0,3,16,12,25,33,7,12,16,43,25,47,49,0,7,55,16,49,64,59,72,7,10,78,35,76,84,86,37,94,96,98,100,102,59,0,111,55</Nodes>
    <FirstSequenceMumOrder>1,2,3,4,5,6,7,8,9</FirstSequenceMumOrder>
    <FirstSequenceStart>31,2,25,15,66,11,0,6,33</FirstSequenceStart>
    <Length>5,7,6,5,5,5,5,5,5</Length>
    <SecondSequenceMumOrder>1,2,3,4,5,6,7,8,9</SecondSequenceMumOrder>
    <SecondSequenceStart>0,10,84,98,101,142,143,191,195</SecondSequenceStart>
    <ExpectedSequences>AAAGGGA,AAAGGGA,CAUUA,CAUUA,CAAAAG,UUUUUG,AUGUU,AUGUU,GAAUGC,GAAUGC,CAAAA,CAAAA,GGAUU,GGAUU,GCAAA,GCAAA,UUACC,UUACC</ExpectedSequences>
  </SimpleAlignRnaNucmerSequence>
  <SimpleAlignMediumSizeSequence>
    <FilePath>TestUtils\Multi_Seq_Medium_Size.fasta</FilePath>
    <SearchSequenceFilePath>TestUtils\Multi_Seq_Search_Medium_Size.fasta</SearchSequenceFilePath>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <GapOpenCost>-10</GapOpenCost>
    <MUMLength>8</MUMLength>
    <MinimumScore>0</MinimumScore>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>8</MUMAlignLength>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>TestUtils\Medium_Size_SimpleAligned_Seq.txt</ExpectedSequences>
  </SimpleAlignMediumSizeSequence>
  <!-- Dna sequence node which is having 1000BP -->
  <SingleDna1000BPSequence>
    <ReferenceSequences>
      <Sequence>GCTGCTGGATGCTGGTTCTCTTTGTGGCCACATGGAGTGACCTGGGCCTCTGCAAGAAGCGCCCGAAGCCTGGAGGATGGAACACTGGGGGCAGCCGATACCCGGGGCAGGGCAGCCCTGGAGGCAACCGCTACCCACCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAAGGAGGTGGCACCCACAGTCAGTGGAACAAGCCGAGTAAGCCAAAAACCAACATGAAGCACATGGCTGGTGCTGCAGCAGCTGGGGCAGTGGTGGGGGGCCTTGGCGGCTACATGCTGGGAAGTGCCATGAGCAGGCCCATCATACATTTCGGCAGTGACTATGAGGACCGTTACTATCGTGAAAACATGCACCGTTACCCCAACCAAGTGTACTACAGGCCCATGGATGAGTACAGCAACCAGAACAACTTTGTGCACGACTGCGTCAATATCACAATCAAGCAGCACACGGTCACCACAACCACCAAGGGGGAGAACTTCACCGAGACCGACGTTAAGATGATGGAGCGCGTGGTTGAGCAGATGTGTATCACCCAGTACGAGAGGGAATCTCAGGCCTATTACCAGAGAGGATCGAGCATGGTCCTCTTCTCCTCTCCACCTGTGATCCTCCTGATCTCTTTCCTCATCTTCCTGATAGTGGGATGAGGAAGGTCTTCCTGTTTTCACCATCTTTCTAATCTTTTTCCAGCTTGAGGGAGGCGGTATCCACCTGCAGCCCTTTTAGTGGTGGTGTCTCACTCTTTCTTCTCTCTTTGTCCCGGATAGGCTAATCAATACCCTTGGCACTGATGGGCACTGGAAAACATAGAGTAGACCTGAGATGCTGGTCAAGCCCCCTTTGATTGAGTTCATCATGAGCCGTTGCTAATGCCAGGCCAGTAAAAGTATAACAGCAA</Sequence>
    </ReferenceSequences>
    <SearchSequences>
      <Sequence>GCTGCTGGATGCTGGTTCTCTTTGTGGCCACATGGAGTGACCTGGGCCTCTGCAAGAAGCGCCCGAAGCCTGGAGGATGGAACACTGGGGGCAGCCGATACCCGGGGCAGGGCAGCCCTGGAGGCAACCGCTACCCACCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAAGGAGGTGGCACCCACAGTCAGTGGAACAAGCCGAGTAAGCCAAAAACCAACATGAAGCACATGGCTGGTGCTGCAGCAGCTGGGGCAGTGGTGGGGGGCCTTGGCGGCTACATGCTGGGAAGTGCCATGAGCAGGCCCATCATACATTTCGGCAGTGACTATGAGGACCGTTACTATCGTGAAAACATGCACCGTTACCCCAACCAAGTGTACTACAGGCCCATGGATGAGTACAGCAACCAGAACAACAAAATGCACGACTGCGTCAATATCACAATCAAGCAGCACACGGTCACCACAACCACCAAGGGGGAGAACTTCACCGAGACCGACGTTAAGATGATGGAGCGCGTGGTTGAGCAGATGTGTATCACCCAGTACGAGAGGGAATCTCAGGCCTATTACCAGAGAGGATCGAGCATGGTCCTCTTCTCCTCTCCACCTGTGATCCTCCTGATCTCTTTCCTCATCTTCCTGATAGTGGGATGAGGAAGGTCTTCCTGTTTTCACCATCTTTCTAATCTTTTTCCAGCTTGAGGGAGGCGGTATCCACCTGCAGCCCTTTTAGTGGTGGTGTCTCACTCTTTCTTCTCTCTTTGTCCCGGATAGGCTAATCAATACCCTTGGCACTGATGGGCACTGGAAAACATAGAGTAGACCTGAGATGCTGGTCAAGCCCCCTTTGATTGAGTTCATCATGAGCCGTTGCTAATGCCAGGCCAGTAAAAGTATAACAGCAA</Sequence>
    </SearchSequences>
    <SearchSequenceAlphabet>Dna</SearchSequenceAlphabet>
    <MUMLength>10</MUMLength>
    <FixedSeparation>0</FixedSeparation>
    <MUMAlignLength>5</MUMAlignLength>
    <MinimumScore>0</MinimumScore>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequences>GCTGCTGGATGCTGGTTCTCTTTGTGGCCACATGGAGTGACCTGGGCCTCTGCAAGAAGCGCCCGAAGCCTGGAGGATGGAACACTGGGGGCAGCCGATACCCGGGGCAGGGCAGCCCTGGAGGCAACCGCTACCCACCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAAGGAGGTGGCACCCACAGTCAGTGGAACAAGCCGAGTAAGCCAAAAACCAACATGAAGCACATGGCTGGTGCTGCAGCAGCTGGGGCAGTGGTGGGGGGCCTTGGCGGCTACATGCTGGGAAGTGCCATGAGCAGGCCCATCATACATTTCGGCAGTGACTATGAGGACCGTTACTATCGTGAAAACATGCACCGTTACCCCAACCAAGTGTACTACAGGCCCATGGATGAGTACAGCAACCAGAACAAC,GCTGCTGGATGCTGGTTCTCTTTGTGGCCACATGGAGTGACCTGGGCCTCTGCAAGAAGCGCCCGAAGCCTGGAGGATGGAACACTGGGGGCAGCCGATACCCGGGGCAGGGCAGCCCTGGAGGCAACCGCTACCCACCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAAGGAGGTGGCACCCACAGTCAGTGGAACAAGCCGAGTAAGCCAAAAACCAACATGAAGCACATGGCTGGTGCTGCAGCAGCTGGGGCAGTGGTGGGGGGCCTTGGCGGCTACATGCTGGGAAGTGCCATGAGCAGGCCCATCATACATTTCGGCAGTGACTATGAGGACCGTTACTATCGTGAAAACATGCACCGTTACCCCAACCAAGTGTACTACAGGCCCATGGATGAGTACAGCAACCAGAACAAC,CAAAA,CAAAA,CAACA,CAACA,ATGCAC,ATGCAC,TGCACGACTGCGTCAATATCACAATCAAGCAGCACACGGTCACCACAACCACCAAGGGGGAGAACTTCACCGAGACCGACGTTAAGATGATGGAGCGCGTGGTTGAGCAGATGTGTATCACCCAGTACGAGAGGGAATCTCAGGCCTATTACCAGAGAGGATCGAGCATGGTCCTCTTCTCCTCTCCACCTGTGATCCTCCTGATCTCTTTCCTCATCTTCCTGATAGTGGGATGAGGAAGGTCTTCCTGTTTTCACCATCTTTCTAATCTTTTTCCAGCTTGAGGGAGGCGGTATCCACCTGCAGCCCTTTTAGTGGTGGTGTCTCACTCTTTCTTCTCTCTTTGTCCCGGATAGGCTAATCAATACCCTTGGCACTGATGGGCACTGGAAAACATAGAGTAGACCTGAGATGCTGGTCAAGCCCCCTTTGATTGAGTTCATCATGAGCCGTTGCTAATGCCAGGCCAGTAAAAGTATAACAGCAA,TGCACGACTGCGTCAATATCACAATCAAGCAGCACACGGTCACCACAACCACCAAGGGGGAGAACTTCACCGAGACCGACGTTAAGATGATGGAGCGCGTGGTTGAGCAGATGTGTATCACCCAGTACGAGAGGGAATCTCAGGCCTATTACCAGAGAGGATCGAGCATGGTCCTCTTCTCCTCTCCACCTGTGATCCTCCTGATCTCTTTCCTCATCTTCCTGATAGTGGGATGAGGAAGGTCTTCCTGTTTTCACCATCTTTCTAATCTTTTTCCAGCTTGAGGGAGGCGGTATCCACCTGCAGCCCTTTTAGTGGTGGTGTCTCACTCTTTCTTCTCTCTTTGTCCCGGATAGGCTAATCAATACCCTTGGCACTGATGGGCACTGGAAAACATAGAGTAGACCTGAGATGCTGGTCAAGCCCCCTTTGATTGAGTTCATCATGAGCCGTTGCTAATGCCAGGCCAGTAAAAGTATAACAGCAA,AATGC,AATGC</ExpectedSequences>
  </SingleDna1000BPSequence>
</AutomationTest>
